[phenixbb] low resolution secondary structure refinement

Nathaniel Echols nechols at lbl.gov
Wed Apr 7 16:52:20 PDT 2010

On Wed, Apr 7, 2010 at 4:38 PM, r n <ramme29 at yahoo.com> wrote:

> I wanted to do low resolution rigid body refinement with secondary
> structural restrain. I have not seen
> any command or information in the phenix document?

Okay, finally writing documentation now.  Sorry!  There isn't actually a
method for combining rigid body refinement with secondary structure
information yet; it would probably be a day or two of work for Pavel or me.
 However, the "morph" option on AutoBuild may do a better job at moving
pieces of that size into place.  (And there are probably other programs
which I haven't used that do something similar.)

You can use the secondary structure restraints with simple coordinate
refinement (strategy individual_sites), by adding
"main.secondary_structure_restraints=True" to the command-line (there is a
corresponding button in the GUI, but only if you have the alpha-test mode
turned on).  Everything else is (in theory) automatic, but if you aren't
using hydrogens, add "h_bond_restraints.substitute_n_for_h=True" as well,
just to be safe.

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